The Kid Who Would Be Pope, Tom and Jack Megan’s musical playing through October 7 at the Theatre at St. Clement’s as part of the New York Musical Theatre Festival is one of those shows that thinks it’s about one thing but is actually about something else. It is, however, so up front about its confusion that you’ll understand it before the opening number concludes. As 11-year-old Billy McPherson (Kyle Brenn) frets about his first day at Catholic school, hollow voices ring out behind him a string of largely disconnected Latin phrases injected solely as laugh-getters — “in flagrante delicto,” sung with full Benedictine fervor, is one prominent lyric. The title of this song as listed in the program? “Ad Nauseum Excelsis.” (Yes, it’s even misspelled!) The name of the school Billy’s worried about fitting into? Our Lady of Perpetual Motion.

That the show is such an obvious-minded turnoff is too bad because, somewhere deep down, there’s the germ of a workable story about a boy struggling to fit into a community he doesn’t understand. The problem is that rather than tell it, the Megans settle for mocking Catholicism as an ends rather than a means. And because they do it without a trace of wit or originality, it’s impossible to derive from it even guilty fun. Billy’s chief faculty adversary, for example, is the authoritarian Sister Rudy, who’s played without layers and without irony by the male actor Eric Anderson. His experience with confession involves a lecherous priest (James Judy) who’s literally slobbering over the thought of Billy’s potential sins. And, oh yes, the school’s musical is, of course, Fiddler on the Roof — but because no one plays the violin, they have to settle for an accordion.

Similarly empty-headed is the central plot. Billy pines for a nun named Sister Katherine (Jillian Louis), who runs around in short shorts and sings much like Julie Andrews did in The Sound of Music (with sweeping samples of that famous score even padding out her vocals), and plans to win her by becoming either the Pope or a saint (the book gets more than a little confused about this) so that he can change Church law and marry Sister Katherine. (I mentioned that Billy is 11 right? Just checking.) By the time Billy gets to the Vatican and discovers that the Pope is a dopey vaudeville caricature (his two songs are titled “A Boy On Dee Loose” and “All Dees Yours!”) rather than a bitter autocrat, you’ve long accepted that this isn’t a musical in the traditional sense, but a ramshackle burlesque built on religious dismissiveness.

Even for a musical running 105 minutes, that’s a flimsy foundation. Because the reasoning for all this is so thin (Sister Katherine doesn’t bother defending her vocation; Billy derives his knowledge of canonization from a book titled So You Want to Be the Pope?) four-fifths of the playing time feels like filler. Worse, large chunks of it — such as Billy’s quest to perform three miracles, including helping a mute sister develop Brooklyn-Jewish-mother speech patterns — throws far too much attention on the idiocy and incuriosity of the lead character we’re supposed to like, care about, and root for. A hole in the center of the hole in the center of the show does not make for effortless, let alone affecting, entertainment. The Megans may have been aiming for whimsical fantasy, but they’ve erred too strongly on the side of stupid.

The kid-heavy cast is fine, with Brenn doing his best and receiving strong help from Rachel Resheff (who was a standout in The People in the Picture on Broadway last season) as Billy’s supportive classmate, Alison; Louis sings decently but can’t overcome her characters cool, dispassionate writing. Gabriel Barre directs (and presumably choreographs, though no one is credited) with as light a touch as anyone involved with this production has. If the lyrics tend to oscillate between forgettable and negligible — the students sing a too-smug primer called “That’s the Parochial Way,” Sister Katherine introduces herself with the strained and unfocused “A New Miraculous Morn,” and the confession number’s rhyming “pigeonhole” with “original” was the only time I ever laughed (if not for the right reasons) — much of the music is cute.

But cute isn’t enough. There must be some dramatic weight or point of view on hand to ground the action and prevent it from playing like a stage-filling sneer. Christopher Durang’s Sister Mary Ignatius Explains It All For You used piercing satire to critique the Church, with hilarious results; Dan Goggin’s Nunsense and its myriad variations tweak little things but are ultimately good-hearted and respectful. Even the Broadway version of Sister Act, which is at least as contemptuous of religion as this show and only slightly more inspired, knows enough to position itself as a delivery vehicle for a catchy Alan Menken–Glenn Slater score.

The Megans would improve things tremendously by not burying their lede. The only times they touch on anything real, or emotionally or dramatic potent, are the quiet moments Billy and Alison share while developing their friendship. The songs here are the best ones, as well, with “Most Boys Are Slobs,” “You Must Begin With An Open Heart,” and “It’s Funny When You’re New” nicely depicting the often nebulous process of finding yourself so you know what you can (and should) present to others. And, not coincidentally, it’s when Billy learns and embraces that that he’s able to discern and pursue what he wants — and abandon what he doesn’t.

Unfortunately, there’s so much dopey detritus piled up all over the place that following this thin but charming strand of story is not easy. If that’s the story the Megans want to tell, then they need to tell it. If they’d prefer to spin a Vatican-vivisecting smarmfest, then they need to go all out (and refresh their gag bag). But because you can’t tell what they want from their story, all you take away from The Kid Who Would Be Pope is a headache.